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- EMDB-17047: Virus-like Particle based on PVY coat protein with RNA-free helic... -

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Basic information

Entry
Database: EMDB / ID: EMD-17047
TitleVirus-like Particle based on PVY coat protein with RNA-free helical architecture
Map dataVLPh sharp symmetric cryoEM map
Sample
  • Complex: Virus-like particle from PVY coat protein
    • Protein or peptide: Genome polyprotein (Fragment)
Keywordshelical / RNA-free / VLP / Potyvirus / PVY / VIRUS LIKE PARTICLE
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein
Function and homology information
Biological speciesPotato virus Y strain NTN
Methodhelical reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsKavcic L / Kezar A / Podobnik M
Funding support Slovenia, 2 items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
Slovenian Research AgencyJ7-7248 Slovenia
CitationJournal: Commun Chem / Year: 2024
Title: From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y.
Authors: Luka Kavčič / Andreja Kežar / Neža Koritnik / Magda Tušek Žnidarič / Tajda Klobučar / Žiga Vičič / Franci Merzel / Ellie Holden / Justin L P Benesch / Marjetka Podobnik /
Abstract: The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid ...The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
History
DepositionApr 7, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17047.png

Downloads & links

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Map

FileDownload / File: emd_17047.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVLPh sharp symmetric cryoEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.259
Minimum - Maximum-1.0551934 - 1.8711836
Average (Standard dev.)0.010193607 (±0.08252501)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17047_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: VLPh raw cryoEM map

Fileemd_17047_additional_1.map
AnnotationVLPh raw cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VLPh half B cryoEM map

Fileemd_17047_half_map_1.map
AnnotationVLPh half B cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VLPh half A cryoEM map

Fileemd_17047_half_map_2.map
AnnotationVLPh half A cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Virus-like particle from PVY coat protein

EntireName: Virus-like particle from PVY coat protein
Components
  • Complex: Virus-like particle from PVY coat protein
    • Protein or peptide: Genome polyprotein (Fragment)

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Supramolecule #1: Virus-like particle from PVY coat protein

SupramoleculeName: Virus-like particle from PVY coat protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The sample contains 3 forms of filaments.
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: Genome polyprotein (Fragment)

MacromoleculeName: Genome polyprotein (Fragment) / type: protein_or_peptide / ID: 1
Details: Due to flexibility, structural model could only be built from H42 to A222.
Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y strain NTN / Strain: NTN
Molecular weightTheoretical: 29.935797 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMDGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE ...String:
GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMDGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSA QSRLFGLDGG IS TQEENTE RHTTEDVSPS MHTLLGVKNM

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Details: 1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 502 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.876 Å
Applied symmetry - Helical parameters - Δ&Phi: -48.107 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1)
Details: cryoSPARC Helical refinement with initial helical parameters from Ab initio model and helical layer lines
Number images used: 27500
Segment selectionNumber selected: 109796 / Software - Name: cryoSPARC (ver. 3.3) / Software - details: Filament tracer / Details: cryosparc filament tracer
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6hxx


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8opb:
Virus-like Particle based on PVY coat protein with RNA-free helical architecture

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